State of the field in multi-omics research: from computational needs to data mining and sharing

M Krassowski, V Das, SK Sahu, BB Misra - Frontiers in Genetics, 2020 - frontiersin.org
Multi-omics, variously called integrated omics, pan-omics, and trans-omics, aims to combine
two or more omics data sets to aid in data analysis, visualization and interpretation to …

Traceability for trustworthy AI: a review of models and tools

M Mora-Cantallops, S Sánchez-Alonso… - Big Data and Cognitive …, 2021 - mdpi.com
Traceability is considered a key requirement for trustworthy artificial intelligence (AI), related
to the need to maintain a complete account of the provenance of data, processes, and …

NeuroKit2: A Python toolbox for neurophysiological signal processing

D Makowski, T Pham, ZJ Lau, JC Brammer… - Behavior research …, 2021 - Springer
NeuroKit2 is an open-source, community-driven, and user-centered Python package for
neurophysiological signal processing. It provides a comprehensive suite of processing …

Raincloud plots: a multi-platform tool for robust data visualization

M Allen, D Poggiali, K Whitaker… - Wellcome open …, 2021 - pmc.ncbi.nlm.nih.gov
Across scientific disciplines, there is a rapidly growing recognition of the need for more
statistically robust, transparent approaches to data visualization. Complementary to this …

[HTML][HTML] The abTEM code: transmission electron microscopy from first principles

J Madsen, T Susi - Open Research Europe, 2021 - ncbi.nlm.nih.gov
Simulation of transmission electron microscopy (TEM) images or diffraction patterns is often
required to interpret experimental data. Since nuclear cores dominate electron scattering …

Visualization of Brain Statistics With R Packages ggseg and ggseg3d

AM Mowinckel, D Vidal-Piñeiro - Advances in Methods and …, 2020 - journals.sagepub.com
There is an increased emphasis on visualizing neuroimaging results in more intuitive ways.
Common statistical tools for dissemination of these results, such as bar charts, lack the …

Appyters: Turning Jupyter Notebooks into data-driven web apps

DJB Clarke, M Jeon, DJ Stein, N Moiseyev… - Patterns, 2021 - cell.com
Jupyter Notebooks have transformed the communication of data analysis pipelines by
facilitating a modular structure that brings together code, markdown text, and interactive …

Ubermag: Toward more effective micromagnetic workflows

M Beg, M Lang, H Fangohr - IEEE Transactions on Magnetics, 2021 - ieeexplore.ieee.org
Computational micromagnetics has become an essential tool in academia and industry to
support fundamental research and the design and development of devices. Consequently …

FISH-quant v2: a scalable and modular tool for smFISH image analysis

A Imbert, W Ouyang, A Safieddine, E Coleno, C Zimmer… - Rna, 2022 - rnajournal.cshlp.org
Regulation of RNA abundance and localization is a key step in gene expression control.
Single-molecule RNA fluorescence in situ hybridization (smFISH) is a widely used single …

[HTML][HTML] NetKet: A machine learning toolkit for many-body quantum systems

G Carleo, K Choo, D Hofmann, JET Smith… - SoftwareX, 2019 - Elsevier
We introduce NetKet, a comprehensive open source framework for the study of many-body
quantum systems using machine learning techniques. The framework is built around a …